{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T18:32:47Z","timestamp":1760985167911},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"24","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation : DNA methylation is an epigenetic change occurring in genomic CpG sequences that contribute to the regulation of gene transcription both in normal and malignant cells. Next-generation sequencing has been used to characterize DNA methylation status at the genome scale, but suffers from high sequencing cost in the case of whole-genome bisulfite sequencing, or from reduced resolution (inability to precisely define which of the CpGs are methylated) with capture-based techniques.<\/jats:p><jats:p>Results : Here we present a computational method that computes nucleotide-resolution methylation values from capture-based data by incorporating fragment length profiles into a model of methylation analysis. We demonstrate that it compares favorably with nucleotide-resolution bisulfite sequencing and has better predictive power with respect to a reference than window-based methods, often used for enrichment data. The described method was used to produce the methylation data used in tandem with gene expression to produce a novel and clinically significant gene signature in acute myeloid leukemia. In addition, we introduce a complementary statistical method that uses this nucleotide-resolution methylation data for detection of differentially methylated features.<\/jats:p><jats:p>Availability : Software in the form of Python and R scripts is available at http:\/\/bioserv.mps.ohio-state.edu\/ premer and is free for non-commercial use.<\/jats:p><jats:p>Contact : pearlly.yan@osumc.edu ; bundschuh@mps.ohio-state.edu<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu583","type":"journal-article","created":{"date-parts":[[2014,9,2]],"date-time":"2014-09-02T00:17:48Z","timestamp":1409617068000},"page":"3567-3574","source":"Crossref","is-referenced-by-count":10,"title":["PrEMeR-CG: inferring nucleotide level DNA methylation values from MethylCap-seq data"],"prefix":"10.1093","volume":"30","author":[{"given":"David E.","family":"Frankhouser","sequence":"first","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Murphy","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James S.","family":"Blachly","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jincheol","family":"Park","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"},{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mike W.","family":"Zoller","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Javkhlan-Ochir","family":"Ganbat","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Curfman","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John C.","family":"Byrd","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shili","family":"Lin","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guido","family":"Marcucci","sequence":"additional","affiliation":[{"name":"1 College of Medicine, Biomedical Sciences Graduate Program, 2 Department of Internal Medicine, Division of Hematology, 3 Department of Statistics, 4 Mathematical Biosciences Institute, 5 Department of Physics, 6 Department of Chemistry & Biochemistry and 7 Center for RNA Biology, The Ohio State University, Columbus, OH 43210, 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